Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007902.1 Hibiscus syriacus cultivar Beakdansim tig00110293_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 611524
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:516784 original size:12 final size:12
Alignment explanation
Indices: 516746--516789 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
516736 TTAATTTTTA
516746 AAAAATATATATT
1 AAAAATAT-TATT
* *
516759 AAAAA-AATACT
1 AAAAATATTATT
516770 AAAAATATTATT
1 AAAAATATTATT
516782 AAAAATAT
1 AAAAATAT
516790 ACTTAATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
11 8 0.31
12 13 0.50
13 5 0.19
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAAATATTATT
Found at i:516795 original size:12 final size:12
Alignment explanation
Indices: 516746--516795 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
516736 TTAATTTTTA
*
516746 AAAAATATATATT
1 AAAAATATA-CTT
*
516759 AAAAAAATAC-T
1 AAAAATATACTT
516770 AAAAATATTA-TT
1 AAAAATA-TACTT
516782 AAAAATATACTT
1 AAAAATATACTT
516794 AA
1 AA
516796 TATATACATG
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
11 9 0.29
12 14 0.45
13 8 0.26
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAAATATACTT
Found at i:520266 original size:24 final size:24
Alignment explanation
Indices: 520232--520278 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
520222 CTGAAACATC
520232 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
520256 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
520279 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:520988 original size:20 final size:20
Alignment explanation
Indices: 520960--521169 Score: 228
Period size: 20 Copynumber: 10.5 Consensus size: 20
520950 AAATTTCAGT
* * * *
520960 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
520980 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
521000 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
521020 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
521040 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
521060 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
521080 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
521100 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
521120 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
521140 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
521160 GTTGCGATTT
1 GTTGCGATTT
521170 TAATATTCGC
Statistics
Matches: 165, Mismatches: 20, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
19 3 0.02
20 159 0.96
21 3 0.02
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:521178 original size:20 final size:20
Alignment explanation
Indices: 521156--521253 Score: 83
Period size: 21 Copynumber: 4.8 Consensus size: 20
521146 ATTTATGTGT
* *
521156 TCGCGTTGCGATTTTAATAT
1 TCGCATTGCGATTTTAATAA
521176 TCGCATTGCGATTTTGGAA-AA
1 TCGCATTGCGATTTT--AATAA
* *
521197 TCGCAATGCGAATTTGTACT-A
1 TCGCATTGCG-ATTT-TAATAA
*
521218 TCGCATTGCGATTTTCAAGAA
1 TCGCATTGCGATTTT-AATAA
*
521239 TCGCGTTGCGATTTT
1 TCGCATTGCGATTTT
521254 GGAAACTGAT
Statistics
Matches: 63, Mismatches: 8, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
19 1 0.02
20 19 0.30
21 36 0.57
22 6 0.10
23 1 0.02
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATTTTAATAA
Found at i:521206 original size:21 final size:21
Alignment explanation
Indices: 521176--521258 Score: 87
Period size: 21 Copynumber: 4.0 Consensus size: 21
521166 ATTTTAATAT
521176 TCGCATTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
521197 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
521218 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
521239 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
521259 CTGATTTGCG
Statistics
Matches: 48, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
20 1 0.02
21 45 0.94
22 2 0.04
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:521249 original size:42 final size:43
Alignment explanation
Indices: 521156--521254 Score: 116
Period size: 42 Copynumber: 2.4 Consensus size: 43
521146 ATTTATGTGT
*
521156 TCGCGTTGCG-ATTT-TAATATTCGCATTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTAATATTCGCATTGCGATTTTGCAAAA
** *
521197 TCGCAATGCGAATTTGTACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTAATATTCGCATTGCGATTTTGCAA-AA
*
521239 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
521255 GAAACTGATT
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
41 10 0.21
42 34 0.71
43 4 0.08
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTAATATTCGCATTGCGATTTTGCAAAA
Found at i:526740 original size:36 final size:36
Alignment explanation
Indices: 526685--526762 Score: 129
Period size: 36 Copynumber: 2.1 Consensus size: 36
526675 AGAGTAATAT
526685 TCCAGTTGCAGACAACAAGGTTTTGATGGAGAAACAA
1 TCCA-TTGCAGACAACAAGGTTTTGATGGAGAAACAA
* *
526722 TCCATTGCAGACACCAAGGTTTTGATGGAGAAAGAA
1 TCCATTGCAGACAACAAGGTTTTGATGGAGAAACAA
526758 TCCAT
1 TCCAT
526763 GAAGAAAACC
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
36 35 0.90
37 4 0.10
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (36 bp):
TCCATTGCAGACAACAAGGTTTTGATGGAGAAACAA
Found at i:529852 original size:17 final size:17
Alignment explanation
Indices: 529830--529868 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
529820 AAATTAGGGA
529830 TTCAAGTAGTTTGAGGT
1 TTCAAGTAGTTTGAGGT
529847 TTCAAGTAGTTTGAGGT
1 TTCAAGTAGTTTGAGGT
529864 TTCAA
1 TTCAA
529869 AACGTTAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.41
Consensus pattern (17 bp):
TTCAAGTAGTTTGAGGT
Found at i:534497 original size:21 final size:20
Alignment explanation
Indices: 534411--534568 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
534401 AAATGACCAA
**
534411 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
534430 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
534450 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
534470 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
534491 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
534512 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
534532 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
534553 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
534569 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:534584 original size:40 final size:40
Alignment explanation
Indices: 534535--534804 Score: 319
Period size: 40 Copynumber: 6.8 Consensus size: 40
534525 CGATTTTCCA
** * ** *
534535 AAATCGCAACGCGAATATGAAAATCGCAACGCGAA-CACAT
1 AAATCGCAACGCGAATCCGTAAATCGCAACGATAATC-CGT
* * * *
534575 AAATCGCAACGTGTATCCGTATATCGCAACGCGT-ATCCGT
1 AAATCGCAACGCGAATCCGTAAATCGCAACG-ATAATCCGT
* *
534615 AAATCGCAATGCGTATCCGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGTAAATCGCAACGATAATCCGT
*
534655 AAATCGCAACGCGTATCCGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGTAAATCGCAACGATAATCCGT
* *
534695 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGTAAATCGCAACGATAATCCGT
* *
534735 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGTAAATCGCAACGATAATCCGT
* * * *
534775 AAATCGCAATGAGAATCTGTAAATCACAAC
1 AAATCGCAACGCGAATCCGTAAATCGCAAC
534805 ACTGAAATTT
Statistics
Matches: 208, Mismatches: 19, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
39 1 0.00
40 206 0.99
41 1 0.00
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.20
Consensus pattern (40 bp):
AAATCGCAACGCGAATCCGTAAATCGCAACGATAATCCGT
Found at i:534600 original size:20 final size:20
Alignment explanation
Indices: 534535--534804 Score: 253
Period size: 20 Copynumber: 13.5 Consensus size: 20
534525 CGATTTTCCA
* ** *
534535 AAATCGCAACGCGAATATGA
1 AAATCGCAACGTGAATCCGT
* *
534555 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGTGAATC-CGT
*
534575 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGTGAATCCGT
* * *
534595 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGTGAATCCGT
* * *
534615 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGTGAATCCGT
534635 AAATCGCAACGAT-AATCCGT
1 AAATCGCAACG-TGAATCCGT
* *
534655 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGTGAATCCGT
534675 AAATCGCAACGAT-AATCCGT
1 AAATCGCAACG-TGAATCCGT
* *
534695 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGTGAATCCGT
534715 AAATCGCAACGAT-AATCCGT
1 AAATCGCAACG-TGAATCCGT
* *
534735 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGTGAATCCGT
534755 AAATCGCAACGAT-AATCCGT
1 AAATCGCAACG-TGAATCCGT
* * *
534775 AAATCGCAATGAGAATCTGT
1 AAATCGCAACGTGAATCCGT
*
534795 AAATCACAAC
1 AAATCGCAAC
534805 ACTGAAATTT
Statistics
Matches: 209, Mismatches: 31, Indels: 20
0.80 0.12 0.08
Matches are distributed among these distances:
20 208 1.00
21 1 0.00
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGTGAATCCGT
Found at i:534797 original size:60 final size:60
Alignment explanation
Indices: 534535--534804 Score: 301
Period size: 60 Copynumber: 4.5 Consensus size: 60
534525 CGATTTTCCA
* ** * * * *
534535 AAATCGCAACGCGAATATGAAAATCGCAACGCGAA-CACATAAATCGCAACG-TGTATCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGAGAATC-CGTAAATCGCAACGAT-AATCCGT
* * * * * *
534595 ATATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
* * * * *
534655 AAATCGCAACGCGTATCCGTAAATCGCAACGATAATCCGTAAATCGCAACGAGAATCTGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
* *
534715 AAATCGCAACGATAATCCGTAAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
* * *
534775 AAATCGCAATGAGAATCTGTAAATCACAAC
1 AAATCGCAACGAGAATCCGTAAATCGCAAC
534805 ACTGAAATTT
Statistics
Matches: 181, Mismatches: 27, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
60 179 0.99
61 2 0.01
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGAGAATCCGTAAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
Found at i:535526 original size:24 final size:24
Alignment explanation
Indices: 535487--535533 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
535477 AAATTTGGTC
535487 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
535511 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
535534 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:538068 original size:33 final size:33
Alignment explanation
Indices: 538031--538101 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
538021 AGAATCGCAA
538031 TGCGAAATGAAAATCGCATTGCGATTCTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTCTCTCGT
** ** **
538064 TGCGATTTTTATTTCGCATTGCGATTCTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTCTCTCGT
538097 TGCGA
1 TGCGA
538102 TTTTCATTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTCTCTCGT
Found at i:538087 original size:19 final size:19
Alignment explanation
Indices: 538063--538140 Score: 103
Period size: 19 Copynumber: 4.4 Consensus size: 19
538053 GATTCTCTCG
*
538063 TTGCGATTTTTATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
538082 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
538096 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
538115 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
538134 TTGCGAT
1 TTGCGAT
538141 AGTCAATTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
14 6 0.12
16 7 0.14
17 6 0.12
19 32 0.63
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:538102 original size:33 final size:33
Alignment explanation
Indices: 538044--538122 Score: 149
Period size: 33 Copynumber: 2.4 Consensus size: 33
538034 GAAATGAAAA
*
538044 TCGCATTGCGATTCTCTCGTTGCGATTTTTATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATT
538077 TCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATT
538110 TCGCATTGCGATT
1 TCGCATTGCGATT
538123 TTCATTTCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.46
Consensus pattern (33 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:538251 original size:33 final size:32
Alignment explanation
Indices: 538199--538360 Score: 139
Period size: 33 Copynumber: 4.8 Consensus size: 32
538189 CCATTACATT
538199 TCGCAATGCGGAAATGAAAATCGCAACGAGATAA
1 TCGCAATGC-GAAATGAAAATCGCAACGAGA-AA
* *
538233 TCGCAATGCGAAATGAAAATCGCAATGCGAAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAAA
* * * *
538265 T-GAAAAT-CGCAACGAGAGAATCGCAATGTGAAATGAAAA
1 TCG-CAATGCGAAATGA-A-AATCGCAA--CG--A-G-AAA
538304 TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGA-AA
*
538337 TCGCAATGCGAAATTAAAATCGCA
1 TCGCAATGCGAAATGAAAATCGCA
538361 TTGCGATTCT
Statistics
Matches: 105, Mismatches: 11, Indels: 25
0.74 0.08 0.18
Matches are distributed among these distances:
31 7 0.07
32 8 0.08
33 53 0.50
34 10 0.10
35 2 0.02
36 1 0.01
38 9 0.09
39 8 0.08
40 7 0.07
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.15
Consensus pattern (32 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:538255 original size:19 final size:19
Alignment explanation
Indices: 538199--538366 Score: 168
Period size: 19 Copynumber: 9.6 Consensus size: 19
538189 CCATTACATT
538199 TCGCAATGCGGAAATGAAAA
1 TCGCAATGC-GAAATGAAAA
*
538219 TCGCAA--CG--A-GATAA
1 TCGCAATGCGAAATGAAAA
538233 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
538252 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
*
538271 TCGCAA--CG--A-GAGAA
1 TCGCAATGCGAAATGAAAA
*
538285 TCGCAATGTGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
538304 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
*
538323 TCGCAA--CG--A-GAGAA
1 TCGCAATGCGAAATGAAAA
*
538337 TCGCAATGCGAAATTAAAA
1 TCGCAATGCGAAATGAAAA
*
538356 TCGCATTGCGA
1 TCGCAATGCGA
538367 TTCTCCCATT
Statistics
Matches: 123, Mismatches: 10, Indels: 31
0.75 0.06 0.19
Matches are distributed among these distances:
14 30 0.24
15 3 0.02
16 5 0.04
17 5 0.04
18 4 0.03
19 70 0.57
20 6 0.05
ACGTcount: A:0.44, C:0.17, G:0.23, T:0.16
Consensus pattern (19 bp):
TCGCAATGCGAAATGAAAA
Found at i:538278 original size:52 final size:52
Alignment explanation
Indices: 538199--538366 Score: 291
Period size: 52 Copynumber: 3.2 Consensus size: 52
538189 CCATTACATT
*
538199 TCGCAATGCGGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAATGAAAA
1 TCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
*
538252 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGTGAAATGAAAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
*
538304 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATTAAAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
*
538356 TCGCATTGCGA
1 TCGCAATGCGA
538367 TTCTCCCATT
Statistics
Matches: 110, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
52 101 0.92
53 9 0.08
ACGTcount: A:0.44, C:0.17, G:0.23, T:0.16
Consensus pattern (52 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
Found at i:538415 original size:19 final size:19
Alignment explanation
Indices: 538373--538472 Score: 147
Period size: 19 Copynumber: 5.5 Consensus size: 19
538363 GCGATTCTCC
538373 CATTGCGATTTTCATTTCCG
1 CATTGCGATTTTCATTT-CG
538393 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
*
538412 CATTGCGA--TTC-TCTCG
1 CATTGCGATTTTCATTTCG
538428 --TTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
538445 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
538464 CATTGCGAT
1 CATTGCGAT
538473 AGTCAATTTT
Statistics
Matches: 73, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.49
20 17 0.23
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (19 bp):
CATTGCGATTTTCATTTCG
Found at i:538469 original size:52 final size:53
Alignment explanation
Indices: 538356--538472 Score: 209
Period size: 53 Copynumber: 2.2 Consensus size: 53
538346 GAAATTAAAA
538356 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
* *
538409 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
538461 TCGCATTGCGAT
1 TCGCATTGCGAT
538473 AGTCAATTTT
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 30 0.48
53 32 0.52
ACGTcount: A:0.15, C:0.25, G:0.17, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:538598 original size:14 final size:14
Alignment explanation
Indices: 538579--538615 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
538569 CATCAATTAC
538579 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
538593 ACAAATCATCTTTT
1 ACAAATCAACTTTT
538607 ACAAATCAA
1 ACAAATCAA
538616 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:540628 original size:33 final size:33
Alignment explanation
Indices: 540577--540669 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
540567 GCGAAACCAA
*
540577 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
* *
540610 AATTGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
540643 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
540670 TGCGATTTTG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:540648 original size:14 final size:14
Alignment explanation
Indices: 540596--540652 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
540586 GCGAAATGAA
*
540596 AATCGCAACGACAG
1 AATCGCAACGAAAG
*
540610 AATTGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
540627 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
540643 AATCGCAACG
1 AATCGCAACG
540653 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 17 0.49
16 5 0.14
17 6 0.17
19 7 0.20
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.12
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:540667 original size:19 final size:19
Alignment explanation
Indices: 540540--540674 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
540530 TAGTTTACTT
* *
540540 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
540560 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
540579 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
540598 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
* *
540612 TTGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
540631 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
540645 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
540664 TCGCAATGCGA
1 TCGCAACGCGA
540675 TTTTGGTTTC
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.46, C:0.23, G:0.19, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:540692 original size:19 final size:19
Alignment explanation
Indices: 540670--540798 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
540660 AAAATCGCAA
540670 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
540689 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
540703 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
540722 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
540736 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
540755 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
540774 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
540794 TGCGA
1 TGCGA
540799 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:540712 original size:33 final size:33
Alignment explanation
Indices: 540670--540761 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
540660 AAAATCGCAA
540670 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
540703 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
540736 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
540762 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:541008 original size:93 final size:93
Alignment explanation
Indices: 540842--541126 Score: 522
Period size: 93 Copynumber: 3.1 Consensus size: 93
540832 TTGAATGGAT
540842 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
540906 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
* *
540934 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTATTATAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
540999 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
541027 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTT--CAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
541090 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
541118 AAATTTACT
1 AAATTTACT
541127 AAGCAATCTA
Statistics
Matches: 187, Mismatches: 5, Indels: 3
0.96 0.03 0.02
Matches are distributed among these distances:
91 52 0.28
92 39 0.21
93 96 0.51
ACGTcount: A:0.46, C:0.18, G:0.12, T:0.23
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:542852 original size:14 final size:14
Alignment explanation
Indices: 542833--542903 Score: 97
Period size: 14 Copynumber: 4.7 Consensus size: 14
542823 TTGAAATGAA
542833 AATCGCAACGAGAG
1 AATCGCAACGAGAG
542847 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
542864 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
542880 AATCGCAACGAGAG
1 AATCGCAACGAGAG
542894 AATCGCAACG
1 AATCGCAACG
542904 CGAAATGAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
14 32 0.62
16 6 0.12
17 6 0.12
19 8 0.15
ACGTcount: A:0.41, C:0.24, G:0.27, T:0.08
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:542870 original size:33 final size:33
Alignment explanation
Indices: 542828--542894 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
542818 TTTGGTTGAA
*
542828 ATGAAAATCGCAACGAGAGAATCGCAACGCGAG
1 ATGAAAATCGCAACGAGAGAATCGCAACGAGAG
*
542861 ATGACAATCGCAACGAGAGAATCGCAACGAGAG
1 ATGAAAATCGCAACGAGAGAATCGCAACGAGAG
542894 A
1 A
542895 ATCGCAACGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.43, C:0.21, G:0.27, T:0.09
Consensus pattern (33 bp):
ATGAAAATCGCAACGAGAGAATCGCAACGAGAG
Found at i:542956 original size:14 final size:14
Alignment explanation
Indices: 542937--542990 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
542927 TTTGGTTTCG
542937 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
542951 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
542970 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
542984 CGTTGCG
1 CGTTGCG
542991 CTTTTCATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
16 3 0.09
17 3 0.09
19 10 0.30
ACGTcount: A:0.07, C:0.26, G:0.24, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:542969 original size:33 final size:33
Alignment explanation
Indices: 542921--543001 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
542911 AAAATCGCAA
**
542921 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
542954 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
*
542987 TGCGCTTTTCATTTC
1 TGCGATTTTCATTTC
543002 TCTCGTTGCG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.07, C:0.23, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:543037 original size:41 final size:41
Alignment explanation
Indices: 542977--543054 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
542967 TCGCGTTGCG
* *
542977 ATTCTCTCGTTGCGCTTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
543018 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
543055 TCTTCTGCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.12, C:0.27, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:543053 original size:21 final size:21
Alignment explanation
Indices: 542978--543053 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
542968 CGCGTTGCGA
*
542978 TTCTCTCGTTGCGCTTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
542999 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
543019 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
543040 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
543054 CTCTTCTGCA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 17 0.37
21 29 0.63
ACGTcount: A:0.11, C:0.26, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:543180 original size:33 final size:33
Alignment explanation
Indices: 543133--543203 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
543123 AATACTAACT
* *
543133 TGAAAATCGGAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
543166 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
543199 TGAAA
1 TGAAA
543204 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:543609 original size:20 final size:20
Alignment explanation
Indices: 543584--543777 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
543574 CTTTAAATAT
543584 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
543604 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
543626 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
543645 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
543665 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
543685 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
543705 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
543725 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
543745 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
543765 CGCGTTGCGATTT
1 CGCGTTGCGATTT
543778 TCGCAATATT
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:543771 original size:60 final size:60
Alignment explanation
Indices: 543584--543777 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
543574 CTTTAAATAT
**
543584 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
543645 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
543705 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
543765 CGCGTTGCGATTT
1 CGCGTTGCGATTT
543778 TCGCAATATT
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:543825 original size:21 final size:21
Alignment explanation
Indices: 543795--543877 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
543785 ATTTTCATAT
*
543795 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
543816 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
543837 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
543858 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
543878 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:547723 original size:14 final size:14
Alignment explanation
Indices: 547706--547736 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
547696 TAAATACGAA
547706 TAATTAATTTAATT
1 TAATTAATTTAATT
*
547720 TAATTAATTTGATT
1 TAATTAATTTAATT
547734 TAA
1 TAA
547737 AATCAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (14 bp):
TAATTAATTTAATT
Found at i:554820 original size:19 final size:19
Alignment explanation
Indices: 554796--554835 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
554786 TGTACATGTG
554796 ATTTTAATAAAATATTTAT
1 ATTTTAATAAAATATTTAT
*
554815 ATTTTAATAAAATGTTTAT
1 ATTTTAATAAAATATTTAT
554834 AT
1 AT
554836 AATATTTATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (19 bp):
ATTTTAATAAAATATTTAT
Found at i:554902 original size:13 final size:13
Alignment explanation
Indices: 554883--554918 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
554873 TACACTTTTC
554883 AAATATTTTAATA
1 AAATATTTTAATA
* *
554896 TAATATTTTGATA
1 AAATATTTTAATA
554909 AAATATTTTA
1 AAATATTTTA
554919 TTTTTATAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (13 bp):
AAATATTTTAATA
Found at i:555093 original size:23 final size:23
Alignment explanation
Indices: 555067--555135 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
555057 TAAAATAAAT
555067 AATTAGGATTTTAGAAATTTGGG
1 AATTAGGATTTTAGAAATTTGGG
* * *
555090 AATTA-GAGTTTTAGGAATTTAGA
1 AATTAGGA-TTTTAGAAATTTGGG
* *
555113 AATTAGGGTTTTATAAATTTGGG
1 AATTAGGATTTTAGAAATTTGGG
555136 GATGTTTTGT
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
22 2 0.06
23 33 0.92
24 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.25, T:0.41
Consensus pattern (23 bp):
AATTAGGATTTTAGAAATTTGGG
Found at i:556083 original size:12 final size:12
Alignment explanation
Indices: 556068--556093 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
556058 CAATATAACC
556068 ATTAATATTTTA
1 ATTAATATTTTA
556080 ATTAATATTTTA
1 ATTAATATTTTA
556092 AT
1 AT
556094 AGATGCTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
ATTAATATTTTA
Found at i:562398 original size:10 final size:10
Alignment explanation
Indices: 562383--562407 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
562373 TATAAATGAA
562383 TTTATTATAT
1 TTTATTATAT
562393 TTTATTATAT
1 TTTATTATAT
562403 TTTAT
1 TTTAT
562408 GTAATTATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTATTATAT
Found at i:569525 original size:2 final size:2
Alignment explanation
Indices: 569518--569543 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
569508 GCTACTAAAA
569518 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
569544 TAAACTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:569797 original size:66 final size:65
Alignment explanation
Indices: 569671--569804 Score: 155
Period size: 66 Copynumber: 2.0 Consensus size: 65
569661 AAACTTCAGC
** * * * *
569671 TTTTTATTTTGAGTAGAGCTTGAAAATTTTAAGCTTGTTAGTTTTCAAGTCGAATTGAGCTTTAA
1 TTTTTATTCCGAGTAGAGCTTGAAAATTTTAAGCTCGTCAGCTTTCAAGTCGAATCGAGC-TTAA
569736 T
65 T
* *
569737 TTTTTATTCCGAGTCGAGCTTGAAAATTTTAAGCTCG-CAGGCTTTCGAGTC-AAGTCGAGCTTA
1 TTTTTATTCCGAGTAGAGCTTGAAAATTTTAAGCTCGTCA-GCTTTCAAGTCGAA-TCGAGCTTA
569800 AT
64 AT
569802 TTT
1 TTT
569805 AAAGTTTTTG
Statistics
Matches: 58, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
65 11 0.19
66 47 0.81
ACGTcount: A:0.25, C:0.13, G:0.19, T:0.43
Consensus pattern (65 bp):
TTTTTATTCCGAGTAGAGCTTGAAAATTTTAAGCTCGTCAGCTTTCAAGTCGAATCGAGCTTAAT
Found at i:569937 original size:3 final size:3
Alignment explanation
Indices: 569929--569956 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
569919 TACTATTCAA
569929 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
569957 TTATTATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:571124 original size:16 final size:17
Alignment explanation
Indices: 571099--571131 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
571089 TCATATGAAT
*
571099 AAAATGAAAAG-AATAA
1 AAAATAAAAAGCAATAA
571115 AAAATAAAAAGCAATAA
1 AAAATAAAAAGCAATAA
571132 TTAAAGGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.76, C:0.03, G:0.09, T:0.12
Consensus pattern (17 bp):
AAAATAAAAAGCAATAA
Found at i:571248 original size:26 final size:25
Alignment explanation
Indices: 571212--571264 Score: 88
Period size: 26 Copynumber: 2.1 Consensus size: 25
571202 ATTAAAGAGC
*
571212 TAAAAAATAAATAACATAAATTAAAA
1 TAAAAAATAAATAAC-TAAAATAAAA
571238 TAAAAAATAAATAACTAAAATAAAA
1 TAAAAAATAAATAACTAAAATAAAA
571263 TA
1 TA
571265 TATCAGAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 11 0.42
26 15 0.58
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.23
Consensus pattern (25 bp):
TAAAAAATAAATAACTAAAATAAAA
Found at i:573388 original size:3 final size:3
Alignment explanation
Indices: 573382--573406 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
573372 TTATTATTTT
573382 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
573407 ATGAGACAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:578206 original size:12 final size:14
Alignment explanation
Indices: 578179--578211 Score: 52
Period size: 12 Copynumber: 2.5 Consensus size: 14
578169 TAAAAATAAA
578179 CATATATATTTATT
1 CATATATATTTATT
578193 CATAT-TATTT-TT
1 CATATATATTTATT
578205 CATATAT
1 CATATAT
578212 GTAAGTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 7 0.39
13 6 0.33
14 5 0.28
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.58
Consensus pattern (14 bp):
CATATATATTTATT
Found at i:585205 original size:37 final size:37
Alignment explanation
Indices: 585154--585231 Score: 131
Period size: 37 Copynumber: 2.1 Consensus size: 37
585144 TTCGTTTGAA
* *
585154 TTGG-TTGTAGTAGATCTCTTGTACTAGTAATTCATT
1 TTGGTTTGTACTAGATCTCTTGTACTAGCAATTCATT
585190 TTGGTTTGTACTAGATCTCTTGTACTAGCAATTCATT
1 TTGGTTTGTACTAGATCTCTTGTACTAGCAATTCATT
585227 TTGGT
1 TTGGT
585232 CAAAGCGATC
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
36 4 0.10
37 35 0.90
ACGTcount: A:0.21, C:0.13, G:0.19, T:0.47
Consensus pattern (37 bp):
TTGGTTTGTACTAGATCTCTTGTACTAGCAATTCATT
Found at i:603576 original size:29 final size:29
Alignment explanation
Indices: 603534--603590 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
603524 AACACTCTAC
603534 GATATTGAGTCGATTATATTATTGTCTTT
1 GATATTGAGTCGATTATATTATTGTCTTT
603563 GATATTGAGTCGATTATATTATTGTCTT
1 GATATTGAGTCGATTATATTATTGTCTT
603591 ATCAATAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.25, C:0.07, G:0.18, T:0.51
Consensus pattern (29 bp):
GATATTGAGTCGATTATATTATTGTCTTT
Found at i:609065 original size:13 final size:14
Alignment explanation
Indices: 609062--609095 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
609052 CGTTTACCCG
*
609062 ACCCGACCCGTTTA
1 ACCCGACCCGTTGA
609076 ACCCGACCCGTTG-
1 ACCCGACCCGTTGA
609089 ACCCGAC
1 ACCCGAC
609096 TCGACTCGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.21, C:0.47, G:0.18, T:0.15
Consensus pattern (14 bp):
ACCCGACCCGTTGA
Found at i:609081 original size:19 final size:19
Alignment explanation
Indices: 609038--609085 Score: 80
Period size: 18 Copynumber: 2.6 Consensus size: 19
609028 GACCGGTCAC
*
609038 AACCCGACCCAACCCGTTT
1 AACCCGACCCGACCCGTTT
609057 -ACCCGACCCGACCCGTTT
1 AACCCGACCCGACCCGTTT
609075 AACCCGACCCG
1 AACCCGACCCG
609086 TTGACCCGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 17 0.63
19 10 0.37
ACGTcount: A:0.23, C:0.50, G:0.15, T:0.12
Consensus pattern (19 bp):
AACCCGACCCGACCCGTTT
Found at i:609085 original size:32 final size:31
Alignment explanation
Indices: 609044--609123 Score: 99
Period size: 32 Copynumber: 2.6 Consensus size: 31
609034 TCACAACCCG
* *
609044 ACCCAACCCGTTTACCCGACCCGACCCGTTTA
1 ACCCGACCCGTTGACCCGACCCGACCCG-TTA
* * *
609076 ACCCGACCCGTTGACCCGACTCGACTCGTTG
1 ACCCGACCCGTTGACCCGACCCGACCCGTTA
609107 A-CCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCG
609124 TTGACCGTTG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
30 16 0.37
31 3 0.07
32 24 0.56
ACGTcount: A:0.19, C:0.45, G:0.19, T:0.17
Consensus pattern (31 bp):
ACCCGACCCGTTGACCCGACCCGACCCGTTA
Found at i:609123 original size:8 final size:8
Alignment explanation
Indices: 609110--609150 Score: 68
Period size: 8 Copynumber: 5.4 Consensus size: 8
609100 CTCGTTGACC
609110 GACCCGTT
1 GACCCGTT
609118 GACCCGTT
1 GACCCGTT
609126 GA-CCGTT
1 GACCCGTT
609133 GACCCGTT
1 GACCCGTT
609141 GA-CCGTT
1 GACCCGTT
609148 GAC
1 GAC
609151 TACTGTTGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 14 0.45
8 17 0.55
ACGTcount: A:0.15, C:0.34, G:0.27, T:0.24
Consensus pattern (8 bp):
GACCCGTT
Found at i:609133 original size:7 final size:7
Alignment explanation
Indices: 609113--609150 Score: 58
Period size: 7 Copynumber: 5.1 Consensus size: 7
609103 GTTGACCGAC
609113 CCGTTGA
1 CCGTTGA
609120 CCCGTTGA
1 -CCGTTGA
609128 CCGTTGA
1 CCGTTGA
609135 CCCGTTGA
1 -CCGTTGA
609143 CCGTTGA
1 CCGTTGA
609150 C
1 C
609151 TACTGTTGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 15 0.52
8 14 0.48
ACGTcount: A:0.13, C:0.34, G:0.26, T:0.26
Consensus pattern (7 bp):
CCGTTGA
Found at i:609133 original size:15 final size:15
Alignment explanation
Indices: 609113--609150 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
609103 GTTGACCGAC
609113 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
609128 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
609143 CCGTTGAC
1 CCGTTGAC
609151 TACTGTTGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.13, C:0.34, G:0.26, T:0.26
Consensus pattern (15 bp):
CCGTTGACCCGTTGA
Done.